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PubMed2005

The formulation of the control of an expression pattern in a gene network by propositional calculus.

In this study we model a gene network as a continuous-time switching network. In this model, each gene has a binary state which indicates if the gene expresses or not. We propose a method to control a sequence of expression patterns in the gene network model by adding another continuous-time switching network. By using propositional calculus, we will show that the control problem can be formulated as a mixed-integer linear programming problem with linear constraints.

Animals↗
PubMed2006

The linear separability problem: some testing methods.

The notion of linear separability is used widely in machine learning research. Learning algorithms that use this concept to learn include neural networks (single layer perceptron and recursive deterministic perceptron), and kernel machines (support vector machines). This paper presents an overview of several of the methods for testing linear separability between two classes. The methods are divided into four groups: Those based on linear programming, those based on computational geometry, one based on neural networks, and one based on quadratic programming. The Fisher linear discriminant method is also presented. A section on the quantification of the complexity of classification problems is included.

Algorithms↗
PubMed1994

A non-linear fitting program in pharmacokinetics with Microsoft Excel spreadsheet.

We propose a new approach of pharmacokinetics patterns of drugs by use of spreadsheets. We have developed a software program using Microsoft Excel (version 3.0) to determine initial poly exponential parameter values for 1-3 compartment open models and to make non-linear regression with many optimisation procedures. Results are compared with 2 other programs: Nonlin and Rugfit.

Administration, Oral↗
PubMed1984

A chance-constrained multiobjective model for mental health services planning.

Mental health services planning, and particularly the planning for deinstitutionalization, is a very complex problem. This paper suggests a chance-constrained goal programming (CCGP) approach to mental health services planning. The CCGP approach is based on the sequential solution of a linear programming formulation, allowing efficient solution of large-scale planning problems using commercially available linear programming computer codes. The procedure is demonstrated with a case example and implementation of the approach is discussed.

Deinstitutionalization↗
PubMed1977

[Computer programming for radiocardiography and radiocyclography].

Digital radiocardiography with linear programming, on the ALGOL language, by means of an ODRA-1204 computer is described. Determination of cardiac dynamical parameters of patients in rest and under load was carried out. Radioisotopic methods were combined with conventional cardiologic examinations, particularly the microcatheterization.

Computers↗
PubMed1999

CARABEAMER: a treatment planner for a robotic radiosurgical system with general kinematics.

Stereotactic radiosurgery is a minimally invasive procedure that uses a focused beam of radiation as an ablative instrument to destroy brain tumors. To deposit a high dose of radiation in a tumor, while reducing the dose to healthy tissue, a large number of beams are crossfired at the tumor from multiple directions. The treatment planning problem (also called the inverse dosimetry problem) is to compute a set of beams that produces the desired dose distribution. So far its investigation has focused on the generation of isocenter-based treatments in which the beam axes intersect at a common point, the isocenter. However this restriction limits the applicability of the treatments to tumors which have simple shapes. This paper describes CARABEAMER, a new treatment planner for a radiosurgical system in which the radiation source can be arbitrarily positioned and oriented by a six-degree-of-freedom manipulator. This planner uses randomized techniques to guess a promising initial set of beams. It then applies space partitioning and linear programming techniques to compute the energy to be delivered along each beam. Finally, it exploits the results of the linear program to iteratively adapt and improve the beam set. Experimental results obtained with CARABEAMER on both patient and synthetic cases are presented and discussed. These results demonstrate that a radiosurgical system with general kinematics can deliver treatments in which the region receiving a high dose closely matches the shape of the tumor, even in complicated cases. They also suggest new research directions which are discussed at the end of the paper.

Algorithms↗
PubMed1998

[Application of constrained simulated annealing to 3D stereotactic radiotherapy treatment planning].

In this paper, linear programming and constrained simulated annealing are combined to optimize X-knife stereotactic radiotherapy treatment planning. In the first phase, linear programming reduces the resolution space, which is favourable to the adoption of little granularity in the second phase. Our experiment demonstrates that after the two-phase optimization, we attain the expected result.

Algorithms↗
PubMed2006

Evaluation of solid waste management strategies in the Taipei metropolitan area of Taiwan.

Municipal solid waste (MSW) management is a major concern for highly urbanized societies. Among proposed MSW management systems, regionalization programs generally have received considerable attention. This study analyzes real-world operational data to assess different MSW management policies, especially regionalization strategies, and their impact on MSW management systems in the Taipei metropolitan area. Linear programming is also used to identify the minimum costs sustained by each policy. The linear programming results show that regionalization programs are more economical and also improve incinerator operation efficiency. Sensitivity analysis indicates that the minimum treatment requirement of incinerators is a very sensitive influence on the MSW flows distributed through the entire region. The MSW of several "sensitive" administrative districts will be allocated to different treatment facilities according to different management strategies. A list of preferential sequences of MSW treatment and disposal facilities can also be identified by the model presented in this study. The results of this study may provide a useful tool for aiding decision-making related to real-world MSW management problems.

Cities↗
PubMed2005

A tree-decomposition approach to protein structure prediction.

This paper proposes a tree decomposition of protein structures, which can be used to efficiently solve two key subproblems of protein structure prediction: protein threading for backbone prediction and protein side-chain prediction. To develop a unified tree-decomposition based approach to these two subproblems, we model them as a geometric neighborhood graph labeling problem. Theoretically, we can have a low-degree polynomial time algorithm to decompose a geometric neighborhood graph G = (V, E) into components with size O(|V|((2/3))log|V|). The computational complexity of the tree-decomposition based graph labeling algorithms is O(|V|Delta(tw+1)) where Delta is the average number of possible labels for each vertex and tw( = O(|V|((2/3))log|V|)) the tree width of G. Empirically, tw is very small and the tree-decomposition method can solve these two problems very efficiently. This paper also compares the computational efficiency of the tree-decomposition approach with the linear programming approach to these two problems and identifies the condition under which the tree-decomposition approach is more efficient than the linear programming approach. Experimental result indicates that the tree-decomposition approach is more efficient most of the time.

Algorithms↗
PubMed1997

Optimal vaccination strategies for a community of households.

The effectiveness of a vaccination program depends on how the vaccinations are spread over the households of the community. Here we formulate the optimal allocation of vaccinations as a linear programming problem, when the objective is to prevent epidemics with the minimum vaccination coverage. A vaccine efficacy of less than 100%, as is usual in practice, is allowed for. Optimal vaccine allocations attempt to leave the same number of susceptibles in every household if the disease has a very high transmission rate within households. This means that proportionately more individuals need to be vaccinated in larger households if the vaccine efficacy is < 100%. The linear programming formulation can accommodate heterogeneity among individuals of the proportionate mixing form and can also minimize the initial reproduction number for a given achievable vaccination coverage.

Communicable Disease Control↗
PubMed1982

Resolution of the multiple inert gas method for estimating VA/Q maldistribution.

During steady-state infusion of a mixture of dissolved inert gases, their elimination by the lung depends on the distribution of ventilation/perfusion (VA/Q) ratios. Thus, certain features of the VA/Q distribution can be inferred from inert gas measurement. Because of the: (1) complexity of the lung, and (2) experimental errors, the ability of such a technique to describe the shape and position of the VA/Q distribution accurately is limited. In this report we present an analysis of the resolution of the method for 9 representative sets of inert gas data, taking account of both of the above factors. These 9 sets span the range of commonly observed data, both in health and in diseases such as asthma, interstitial fibrosis, chronic obstructive lung disease and respiratory distress syndromes. Both error-free and error-containing data are studied and by linear programming methods, bounds are placed on maximum and minimum possible perfusion in several regions of the VA/Q spectrum. Modality is also studied by linear programming. The results show that the resolving power of the method depends greatly on the specific case under study. When groups of units are separated in VA/Q by a decade, this can be determined with considerable confidence. Shunt and low VA/Q areas can generally be well resolved, but when distributions are very broad, resolution is limited.

Aging↗
PubMed2002

A combinatorial toolbox for protein sequence design and landscape analysis in the grand canonical model.

In modern biology, one of the most important research problems is to understand how protein sequences fold into their native 3D structures. To investigate this problem at a high level, one wishes to analyze the protein landscapes, i.e., the structures of the space of all protein sequences and their native 3D structures. Perhaps the most basic computational problem at this level is to take a target 3D structure as input and design a fittest protein sequence with respect to one or more fitness functions of the target 3D structure. We develop a toolbox of combinatorial techniques for protein landscape analysis in the Grand Canonical model of Sun, Brem, Chan, and Dill. The toolbox is based on linear programming, network flow, and a linear-size representation of all minimum cuts of a network. It not only substantially expands the network flow technique for protein sequence design in Kleinberg's seminal work but also is applicable to a considerably broader collection of computational problems than those considered by Kleinberg. We have used this toolbox to obtain a number of efficient algorithms and hardness results. We have further used the algorithms to analyze 3D structures drawn from the Protein Data Bank and have discovered some novel relationships between such native 3D structures and the Grand Canonical model.

Algorithms↗
PubMed2004

Assigning cells to switches in cellular networks by incorporating a pricing mechanism into simulated annealing.

Handoff and cabling costs play key roles in the design of cellular telecommunications networks. Efficient homing of cells to switches can have a significant impact on each of these costs. In the presence of capacity constraints at the switches, the problem of assigning cells to switches becomes a difficult one to solve, with all effective solution approaches being based on heuristic techniques. This paper presents a hybrid heuristic which integrates ideas from linear programming into a simulated annealing framework. Extensive computational results are presented comparing the performance of the heuristic with the lower bound obtained from the linear programming relaxation. These results indicate that this price influenced simulated annealing (PISA) procedure is extremely efficient, usually providing solutions with gaps around 1% in less than 1 s.

Journal Article↗
PubMed1975

Impact of expanded-duty assistants on cost and productivity in dental care delivery.

Data from an experimental dental program are used to develop a linear programming model of dental care delivery that the authors use to examine the economic implications of introducing expanded-duty dental assistants (EDDA's) in three types of dental practices. The authors examine the changes in productivity and profitability that result from hiring one or more EDDAs and conclude that a dentist in solo practice can more than double his net revenue by hiring one EDDA but will not increase his productivity further by hiring additional EDDAs. Two- and three-dentist groups also can increase revenue by hiring EDDAs, but, beyond a certain point, an inverse relationship exists between the number of auxiliaries hired and net revenue generated.

Cost-Benefit Analysis↗
PubMed1977

Evaluation of a self-instructional unit for use in educational programs in histologic technique.

A linear programmed instructional booklet was developed and used to evaluate the acceptability of this learning strategy to histologic technique instructors and their students. Comparisons of students' cognitive knowledge of the relevant topics before and after using the booklet indicated that most were achieving the booklet's objectives. The post-test score was not significantly affected either by prior experience with programmed materials or by the way the booklet was used. The verbal attitude responses of the students were encouraging, and most indicated the booklet was an efficient way for them to learn, and it was helpful in clarifying concepts. The verbal attitudes of the instructors were also favorable. The indications were that booklet use shortened subsequent lecture time and that the booklet was most valuable as a supplement to conventional instructional methods.

Achievement↗
PubMed2002

[The use of operation research tools as a way of more effective utilization of the resources of health service institutions].

In all aspects of human life including medical we can find planning, organizing and controlling of activity. We aim at the proper goal supported by our resources and knowledge. Often we cannot make a decision freely because of surrounding circumstances: economic, organizational, political and others. Taking into account our goals some decisions are good, others are bad. The problem is how to make the best decision. Nowadays, statistical and mathematical tests are widely used in economy. One of the sciences concerned with in evaluating managers' decisions is operations research. Summing up, operations research deals with the problem of how to gain means and use resources in the most effective way taking into account surrounding limitations. As an example of a place where one of the operations research tools (linear programming) is used as a way of work optimalization is Medical Rehabilitation Unit in John Paul II Hospital in Zamość. It is a method in which goal function (that is criterion of optimalization) and limitations are linear functions. The problem is to find a solution (regarding limitations) so that the goal function has the greatest value. The aim of the study is to present and encourage managers to use linear programming as a way of improving effectiveness and disclosing weak points of organization.

Decision Making, Organizational↗
PubMed1982

The contributions of Jerome Cornfield to the theory of statistics.

This paper is a review of the contributions of Jerome Cornfield to the theory of statistics. It discusses several highlights of his theoretical work as well as describing his philosophy relating theory to application. The three areas discussed are: linear programming, urn sampling and its generalizations to the analysis of variance, and Bayesian inference. It is not widely known that Jerome Cornfield was perhaps the first to formulate and approximately solve the linear programming problem in 1941. His formulation was made for the famous "Diet Problem". An early publication introduced the method of indicator random variables in the context of urn sampling. This simple method allowed straightforward calculations of the low order moments for estimates arising from sampling finite populations and was later generalized to the two-way analysis of variance. The application of the urn sampling model to the analysis of variance served to illuminate how one chooses proper error terms for making tests in the analysis of variance table. Jerome Cornfield's philosophy on applications of statistics was dominated by a Bayesian outlook. His theoretical contributions in the past two decades were mainly concerned with the development of Bayesian ideas and methods. A brief survey is made of his main contributions to this area. A particularly noteworthy result was his demonstration that for the two-sample slippage problem of location, the likelihood function under a permutation setting is uninformative for the slippage parameter. However, the posterior distribution differs from the prior distribution despite the fact that the likelihood is uninformative.

Bayes Theorem↗
PubMed2006

Resampling: an optimization method for inverse planning in robotic radiosurgery.

By design, the range of beam directions in conventional radiosurgery are constrained to an isocentric array. However, the recent introduction of robotic radiosurgery dramatically increases the flexibility of targeting, and as a consequence, beams need be neither coplanar nor isocentric. Such a nonisocentric design permits a large number of distinct beam directions to be used in one single treatment. These major technical differences provide an opportunity to improve upon the well-established principles for treatment planning used with GammaKnife or LINAC radiosurgery. With this objective in mind, our group has developed over the past decade an inverse planning tool for robotic radiosurgery. This system first computes a set of beam directions, and then during an optimization step, weights each individual beam. Optimization begins with a feasibility query, the answer to which is derived through linear programming. This approach offers the advantage of completeness and avoids local optima. Final beam selection is based on heuristics. In this report we present and evaluate a new strategy for utilizing the advantages of linear programming to improve beam selection. Starting from an initial solution, a heuristically determined set of beams is added to the optimization problem, while beams with zero weight are removed. This process is repeated to sample a set of beams much larger compared with typical optimization. Experimental results indicate that the planning approach efficiently finds acceptable plans and that resampling can further improve its efficiency.

Computer Simulation↗